[MINC-development] hdf attribute size

[Soren Christensen]

Thanks, I will have a look at that - is that in dcm2mnc?

Soren


On Sun, Oct 13, 2013 at 1:33 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Soren,
>
> No I haven't hit the limit yet but given the amount you are trying to
> stuff in you probably should be using a data variable for this instead
> of the data definition (attribute).
>
> An existing example of how this is done in MINC would be the slice
> time position variable for MINC files with irregular spacing. There
> are text/string HDF datatypes so in my mind this would be the best
> long-term solution for this.
>
>
> a
>
>
> On 12 October 2013 14:56, Soren Christensen <sorench at gmail.com> wrote:
> > Hi,
> >  Has anyone else had problems with the 64kb limit on attributes in the
> > minc-header?
> > I am storing a slice-time matrix of values from the originating DICOM
> files
> > in order to not loose information from some key DICOM attributes.
> > Often I will have thounsands of DICOMs going into one MINC file. For
> > attributes that are uniform accross all DICOMs I just write the atreibute
> > once, but for varying attributes I fill in the above slice-time matrix.
> So
> > for thousands of files this get pretty big. AcquisitionDateTime for
> example
> > will take more bytes to store than 64kb. I use strings only for header
> > items.
> > So I get errors like these from hdf (via miset_attr_values):
> >
> > HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
> >
> > #000:
> /home/s/CODE/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Adeprec.c
> > line 165 in H5Acreate1(): unable to create attribute
> >
> > major: Attribute
> >
> > minor: Unable to initialize object
> >
> > #001: /home/s/CODE/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5A.c line
> > 496 in H5A_create(): unable to create attribute in object header
> >
> > major: Attribute
> >
> > minor: Unable to insert object
> >
> > #002:
> > /home/s/CODE/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Oattribute.c
> line
> > 346 in H5O_attr_create(): unable to create new attribute in header
> >
> > major: Attribute
> >
> > minor: Unable to insert object
> >
> > #003:
> /home/s/CODE/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Omessage.c
> > line 224 in H5O_msg_append_real(): unable to create new message
> >
> > major: Object header
> >
> > minor: No space available for allocation
> >
> > #004:
> /home/s/CODE/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Omessage.c
> > line 1925 in H5O_msg_alloc(): unable to allocate space for message
> >
> > major: Object header
> >
> > minor: Unable to initialize object
> >
> > #005: /home/s/CODE/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Oalloc.c
> > line 1136 in H5O_alloc(): object header message is too large
> >
> > major: Object header
> >
> > minor: Unable to initialize object
> >
> > problem with key: "AcquisitionDateTime"
> >
> >
> > Does anyone know of an easy workaround for this?
> >
> > It seems one can change the hdf call quite easily to do away with this
> 64kb
> > limitation, but I am not sure of any potential penalties. An optimistic
> > interpretation of the below document says it will be more efficient and
> is
> > simply a new feature of hdf 1.8. (inserting new header items I suppose).
> > http://www.hdfgroup.org/HDF5/doc/UG/13_Attributes.html (see 8.5)
> > Compatibility with hdf<1.8 would be lost
> >
> > So I suppose one could make an miset_attr_values_large or somehow
> optionally
> > create a dense group? Or perhaps replace the setup with "dense" groups
> (see
> > hdf document), provided it provides appropriate backwards file
> > compatibility?
> >
> > I'd like to pursue this when I get more time available, but maybe someone
> > well versed in hdf could chime in?
> >
> > Thanks
> > Soren
> >
> >
> >
> > _______________________________________________
> > MINC-development mailing list
> > MINC-development at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> >
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